Closed giampe79 closed 7 years ago
Hi Annalisa,
I'm happy to report that this bug has been fixed! https://github.com/rrwick/Unicycler/commit/c97159770522fb42fc749998350a81698870f273
The first (and simplest) solution would be to just run a more recent version of Unicycler through Docker:
docker run quay.io/biocontainers/unicycler:0.3.0b--py35_0 unicycler
I've updated the Unicycler README to show this one instead of the previous version (0.2.0) which still has the bug. However, this version isn't completely up-to-date. I've submitted an updated recipe to BioConda for the new version I just made (v0.3.0), but I must confess that I'm not very savvy with this Bioconda/BioContainers stuff.
Alternatively, you could clone and install Unicycler yourself, without Docker. This will let you get the most recent version, but you'll have to make sure you have all the other dependencies installed, like SPAdes.
Ryan
Dear Unicycler author, I have tried Unicycler tool to assemble my genome (2,5 milion base) with a set of paired Illumina reads and a set of PacBio reads, I have used the docker container to run it. The run of command failed , I;m reporting below the relative message, Could you help me to fix these errors? COMMAND LAUNCHED: c1780c8c[unicycler_input_result]# unicycler -1 RAMS001_dd_S28_L004_R1_001.fastq -2 RAMS001_dd_S28_L004_R2_001.fastq -l R125-G01.1-Reads.fastq -o ./output_dirUnicycler --pilon_path=/usr/local/share/pilon-1.20-0/pilon-1.20.jar
REPORT Starting Unicycler Command: /usr/local/bin/unicycler -1 RAMS001_dd_S28_L004_R1_001.fastq -2 RAMS001_dd_S28_L004_R2_001.fastq -l R125-G01.1-Reads.fastq -o ./output_dirUnicycler --pilon_path=/usr/local/share/pilon-1.20-0/pilon-1.20.jar
Making output directory: /home/unicycler_input_result/output_dirUnicycler
SPAdes read error correction Command: /usr/local/bin/spades.py -1 /home/unicycler_input_result/RAMS001_dd_S28_L004_R1_001.fastq -2 /home/unicycler_input_result/RAMS001_dd_S28_L004_R2_001.fastq -o /home/unicycler_input_result/output_dirUnicycler/spades_assembly_temp/read_correction --threads 8 --only-error-correction
Corrected reads: /home/unicycler_input_result/output_dirUnicycler/spades_assembly_temp/corrected_1.fastq.gz /home/unicycler_input_result/output_dirUnicycler/spades_assembly_temp/corrected_2.fastq.gz /home/unicycler_input_result/output_dirUnicycler/spades_assembly_temp/corrected_u.fastq.gz
Choosing k-mer range for assembly Median read length: 151 K-mer range: 27, 47, 63, 77, 89, 99, 107, 115, 121, 127
Conducting SPAdes assemblies K-mer Segments Dead ends Score 27 too complex 47 too complex 63 325 0 3.08e-03 77 260 0 3.85e-03 89 178 0 5.62e-03 99 157 0 6.37e-03 107 139 0 7.19e-03 115 124 0 8.06e-03 121 115 0 8.70e-03 Traceback (most recent call last): File "/usr/local/bin/unicycler", line 11, in
load_entry_point('unicycler==0.2.0', 'console_scripts', 'unicycler')()
File "/usr/local/lib/python3.5/site-packages/unicycler/unicycler.py", line 79, in main
args.expected_linear_seqs)
File "/usr/local/lib/python3.5/site-packages/unicycler/spades_func.py", line 152, in get_best_spades_graph
row_extra_text={best_kmer_row: ' \u2190 best'})
File "/usr/local/lib/python3.5/site-packages/unicycler/misc.py", line 628, in print_table
print(indenter + row_str, flush=True)
UnicodeEncodeError: 'ascii' codec can't encode character '\u2190' in position 48: ordinal not in range(128)
c1780c8c[unicycler_input_result]#
thanks in advance Annalisa